Contacts of the helix formed by residues 41 - 63 (chain C) in PDB entry 5H15
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 41 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 4.7 13.0 - - + -
332A LYS* 3.8 19.1 - - - +
336A MET* 3.5 39.7 - - + +
337A GLU* 5.1 4.0 - - - -
353A LEU* 3.6 35.2 - - + -
40C SER* 1.3 71.9 - - - +
42C PHE* 1.4 56.7 + - - +
44C SER* 3.9 5.9 - - - +
45C ASN* 3.0 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 5.9 2.5 - - - -
391A LEU 3.5 17.7 - - - -
392A GLU 3.4 32.5 - - - -
393A VAL 4.3 0.7 - - - -
394A GLU* 3.5 61.2 + - + +
40C SER* 3.3 3.9 - - - +
41C MET* 1.4 75.5 - - - +
43C SER* 1.4 60.9 + - - +
45C ASN* 3.2 7.0 + - + +
46C ARG* 2.8 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER* 3.0 28.9 + - - -
42C PHE* 1.4 83.3 - - - +
44C SER* 1.3 57.4 + - - +
46C ARG* 3.3 9.0 + - - +
47C GLN* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER 3.3 17.1 + - - -
41C MET* 3.9 8.2 - - - +
43C SER* 1.3 80.2 + - - +
45C ASN* 1.3 61.2 + - - +
47C GLN* 3.2 8.7 + - - +
48C LYS* 3.2 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 2.9 21.3 + - - +
316A GLY* 3.5 3.6 - - - -
317A ASP* 2.9 37.0 - - - +
318A LEU* 3.4 29.8 - - + +
41C MET* 3.0 19.8 + - + +
42C PHE* 3.6 4.7 - - - +
44C SER* 1.3 74.8 + - - +
46C ARG* 1.4 56.3 + - + +
48C LYS* 3.2 14.9 + - - +
49C ILE* 3.0 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 3.9 7.9 - - - +
373A TRP 4.1 3.4 + - - -
374A GLN 2.7 32.1 + - - -
375A LYS* 4.3 4.6 - - - +
391A LEU* 3.5 30.5 + - - +
392A GLU* 3.9 27.8 + - - +
42C PHE* 2.8 45.5 + - + +
43C SER* 3.4 9.9 - - - +
44C SER 3.3 0.2 - - - -
45C ASN* 1.4 75.2 - - - +
47C GLN* 1.3 56.8 + - - +
49C ILE* 3.6 40.7 + - - +
50C LEU* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C SER 3.1 12.8 + - - +
44C SER* 3.2 10.1 + - - +
46C ARG* 1.3 72.6 - - - +
48C LYS* 1.4 55.8 + - - +
50C LEU* 3.4 29.0 - - - +
51C GLU* 2.8 73.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLY* 4.8 3.1 - - - -
317A ASP* 2.9 35.3 + - - +
339A ASP* 5.5 2.2 + - - -
44C SER* 3.2 30.1 + - - +
45C ASN* 3.3 21.2 - - - +
47C GLN* 1.4 71.5 - - - +
49C ILE* 1.3 59.6 + - - +
51C GLU* 3.3 5.2 + - - +
52C ARG* 2.9 68.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.9 9.0 - - - -
315A LEU* 3.9 15.7 - - + -
316A GLY* 3.6 20.6 - - - +
373A TRP 3.7 22.4 - - - +
374A GLN* 3.6 20.2 - - + +
45C ASN* 3.0 35.2 + - - +
46C ARG* 3.6 43.3 - - - +
48C LYS* 1.3 73.5 - - - +
50C LEU* 1.4 53.8 + - - +
53C THR* 2.8 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A TRP* 4.6 12.9 - - + -
375A LYS* 5.7 8.5 - - - +
46C ARG 2.9 18.9 + - - +
47C GLN* 3.4 33.9 - - - +
48C LYS 3.3 0.2 - - - -
49C ILE* 1.4 76.1 - - - +
51C GLU* 1.3 61.9 + - + +
53C THR* 3.4 5.8 + - - -
54C GLU* 3.0 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLN* 2.8 50.9 + - - +
48C LYS* 3.7 5.4 - - - +
50C LEU* 1.3 72.3 - - + +
52C ARG* 1.3 61.8 - - + +
54C GLU* 3.4 7.8 + - - +
55C ILE* 3.2 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 5.5 5.1 + - - +
246A LEU* 3.8 30.3 - - + -
247A LEU* 4.0 35.0 - - + +
250A LYS* 5.5 2.0 - - - +
316A GLY 4.5 8.5 + - - -
317A ASP* 3.0 27.9 + - - -
48C LYS* 2.9 54.3 + - - +
51C GLU* 1.3 77.1 - - + +
53C THR* 1.4 63.5 + - - +
54C GLU 3.2 0.2 - - - -
55C ILE* 3.2 12.2 + - + +
56C LEU* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.6 27.1 - - + -
372A PHE* 3.5 28.3 - - + +
373A TRP* 3.1 33.0 + - - +
374A GLN* 4.6 2.2 - - + -
49C ILE* 2.8 41.3 + - + +
50C LEU* 3.4 4.5 + - - -
52C ARG* 1.4 68.9 - - - +
54C GLU* 1.4 54.9 + - - +
56C LEU* 3.3 7.0 + - - -
57C ASN* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A TRP* 3.6 21.2 - - + -
50C LEU* 3.0 22.3 + - + +
51C GLU* 3.5 7.9 - - - +
53C THR* 1.4 73.6 + - - +
55C ILE* 1.3 58.5 + - + +
57C ASN* 3.2 6.7 + - - +
58C GLN* 2.9 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ARG* 3.6 32.3 - - - +
247A LEU* 4.3 21.5 - - + -
51C GLU* 3.2 17.4 + - + +
52C ARG* 3.2 11.4 + - + +
54C GLU* 1.3 75.8 - - + +
56C LEU* 1.4 62.8 + - + +
58C GLN* 3.3 6.6 + - - +
59C GLU* 3.2 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PRO* 4.1 20.9 - - + +
201A ARG* 3.6 33.2 - - - +
246A LEU* 3.6 44.2 - - + +
247A LEU* 4.9 1.3 - - + -
372A PHE* 3.9 22.7 - - + -
420A ARG* 4.2 1.0 + - - +
52C ARG 3.1 13.4 + - - +
53C THR* 3.3 7.2 + - - +
55C ILE* 1.4 76.2 - - + +
57C ASN* 1.3 57.6 + - - +
59C GLU* 3.3 10.4 + - - +
60C TRP* 3.1 28.9 + - - +
63C ARG* 4.3 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 3.6 7.0 - - + -
373A TRP* 3.5 31.7 + - + -
420A ARG* 3.4 21.9 + - - +
53C THR 2.8 21.2 + - - +
54C GLU* 3.6 11.9 + - - +
56C LEU* 1.3 72.7 - - - +
58C GLN* 1.4 55.8 + - - +
60C TRP* 3.4 16.5 + - - +
61C LYS* 3.0 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 2.9 41.2 + - + +
55C ILE* 3.3 7.2 + - - +
57C ASN* 1.4 75.0 - - - +
59C GLU* 1.3 64.1 + - + +
61C LYS* 3.2 40.4 + - - +
62C GLN* 3.2 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PRO 4.6 1.9 - - - +
201A ARG* 3.0 53.5 + - - +
55C ILE* 3.2 18.6 + - + +
56C LEU* 3.6 13.1 - - - +
58C GLN* 1.3 75.0 - - + +
60C TRP* 1.3 63.7 + - - +
62C GLN* 3.5 10.6 + - - +
63C ARG* 3.4 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP 3.3 21.0 + - - -
104A HIS 3.4 8.1 + - - -
105A SER 3.2 28.3 + - - -
106A LYS* 4.0 3.9 - - - +
107A GLU* 3.6 44.9 - - + -
420A ARG* 3.3 38.8 - - - +
56C LEU 3.1 10.6 + - - +
57C ASN* 3.6 31.4 - - - +
59C GLU* 1.3 75.7 - - - +
61C LYS* 1.4 82.7 + - + +
63C ARG* 3.2 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 5.5 6.7 - - - +
57C ASN* 3.0 35.1 + - - +
58C GLN* 3.2 34.9 + - - +
60C TRP* 1.4 92.7 - - + +
62C GLN* 1.3 57.8 + - - +
63C ARG 3.6 0.3 - - - +
64C ARG* 2.7 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LYS* 4.9 9.7 + - - -
58C GLN* 3.2 42.4 + - - +
59C GLU* 3.9 9.0 - - - +
60C TRP 3.4 0.2 - - - -
61C LYS* 1.3 79.2 - - - +
63C ARG* 1.3 60.9 + - + +
64C ARG* 3.9 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A HIS* 3.2 31.9 + - - +
106A LYS* 4.5 8.5 - - - +
154A TYR* 3.4 40.3 + - + -
159A SER* 6.0 0.2 - - - +
200A PRO 5.1 8.1 + - - -
420A ARG* 5.5 2.0 - - - +
275B LYS* 6.2 0.2 - - - +
56C LEU 4.3 4.8 + - - -
59C GLU* 3.4 19.9 + - - +
60C TRP* 3.2 63.7 + - + +
61C LYS 3.6 0.3 - - - +
62C GLN* 1.3 79.8 - - + +
64C ARG* 1.3 75.0 + - - +
65C ILE* 3.8 19.1 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il